Institution
Nancy-Université
Education•
About: Nancy-Université is a based out in . It is known for research contribution in the topics: Population & Magnetization. The organization has 7096 authors who have published 9965 publications receiving 314936 citations. The organization is also known as: University of Nancy & Nancy-Universite.
Topics: Population, Magnetization, Adsorption, Nonlinear system, Catalysis
Papers published on a yearly basis
Papers
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TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
14,558 citations
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TL;DR: These guidelines include recommendations for obtaining semantic, idiomatic, experiential and conceptual equivalence in translation by using back-translation techniques and committee review, pre-testing techniques and re-examining the weight of scores.
5,114 citations
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TL;DR: This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
Abstract: phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
4,380 citations
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TL;DR: In this article, the topological properties of ρ(r) at the intermolecular critical points of 83 experimentally observed hydrogen bonds [X-H⋯O (X=C,N,O)], using accurate X-ray diffraction experiments, were analyzed.
2,675 citations
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TL;DR: It is demonstrated that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes.
Abstract: Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes.
2,022 citations
Authors
Showing all 7099 results
Name | H-index | Papers | Citations |
---|---|---|---|
Martin Karplus | 163 | 831 | 138492 |
Klaus Schulten | 147 | 770 | 137523 |
Jean-Frederic Colombel | 147 | 1125 | 98944 |
David Brown | 105 | 1257 | 46827 |
Francis Martin | 98 | 733 | 43991 |
Dante Gatteschi | 97 | 727 | 48729 |
Muhammad Imran | 94 | 3053 | 51728 |
Laurent Peyrin-Biroulet | 90 | 901 | 34120 |
Richard Casaburi | 89 | 392 | 55362 |
Jérôme Bertherat | 85 | 438 | 24794 |
Athanase Benetos | 83 | 391 | 31718 |
Andrea Caneschi | 80 | 435 | 25896 |
Christian Amatore | 80 | 585 | 25487 |
François Béguin | 75 | 344 | 30660 |
Xavier Bertagna | 74 | 285 | 18738 |